Present techniques to detect chromosomal breakpoint locations at a molecular level utilize Southern blotting or direct sequencing and cloning of DNA. A limitation of Southern blotting is that it requires a greater amount of tumor sample in order to analyze the DNA and multiple digestions with restriction endonucleases are necessary. Moreover, the results from the tests need to be compared with control samples, a process which is subjective and can, on occasion, lead to error.
Other techniques, such as direct sequencing and cloning of the DNA are cumbersome and time consuming. Cytogenetic analysis does not provide identification of the breakpoint locations at a molecular level and is relatively insensitive. Flow cytometry requires a larger number of cells for analysis and suffers from the disadvantage that with the exception of anti-idiotype markers, no truly tumor specific marker detectable by this technique exists. Until now, the most precise means of identifying breakpoint locations has been molecular cloning, but this method is too cumbersome for routine clinical use or for the analysis of a large number of tumors. Southern blotting is more practical. However, for the reasons stated above, Southern blotting does not provide much greater sensitivity than microscopy.